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IntaRNA 3751556

Input and runtime details for job 3751556 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_000913
? All repliconsyes
? Extract sequences aroundstart codon
? nt upstream (1-300)75
? nt downstream (1-300)75
? Index first target position-75

Output Parameters

? Number of interactions per RNA pair1
? Suboptimal interaction overlap can overlap in query
? Max. interaction lengthnot provided
? Max. absolute energy of an interaction0
? Max. delta energy above mfe of an interaction100
? No lonely base pairsyes
? No GU at helix endsyes

Seed Parameters

? Min. number of basepairs in seed7
? Max. Number of mismatches in seed0
? Maximal energy0
? Minimal unpaired probability (per RNA)0
? Seed position (query)not provided
? Seed position (target)not provided
? Ignore seeds with GU base pairsno
? Ignore seeds with GU endsyes

Folding Parameters

? Temperature for energy computation37.0
? Access. query: folding window size150
? Access. query: max. basepair distance100
? Access. target: folding window size150
? Access. target: max. basepair distance100
? Energy parameter set (Vienna package) Turner model, 2004

Job ID 3751556 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:09:18 CET 2020
?IntaRNA Started@ Mon Jan 27 14:12:06 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:12:59 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:14:52 CET 2020
?Job Completed@ Mon Jan 27 14:15:02 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3751556&toolName=IntaRNA ( 30 days expiry )

Description of the job

CyaR - E. coli

? Output [zip]

Downloadable files

[csv]
[png] [pdf]
[png] [pdf]
[txt]
[html] [pdf] [png]


heatmap

? Identified Interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Sort by selecting a column name.
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
b2077 26 54 CyaR 1 30 -18.84 0.0001018 0.2119128 iceT putative citrate/iron-citrate/zinc-citrate efflux transporter
b4074 -70 -57 CyaR 35 48 -18.4 0.0001518 0.2119128 nrfE heme lyase (NrfEFG) for insertion of heme into c552 subunit NrfE
b1485 -11 12 CyaR 25 49 -16.69 0.0006365 0.4585162 ddpC DD-dipeptide ABC transporter permease
b2039 31 74 CyaR 2 46 -16.65 0.0006569 0.4585162 rfbA glucose-1-phosphate thymidylyltransferase
b1498 53 75 CyaR 21 44 -16.06 0.0010357 0.5783349 ydeN putative Ser-type periplasmic non-aryl sulfatase
b1686 60 73 CyaR 35 49 -15.77 0.0012872 0.5989771 menI 14-dihydroxy-2-naphthoyl-CoA hydrolase
b1209 -57 -34 CyaR 11 36 -15.14 0.0020364 0.7364947 lolB lipoprotein localization factor
b2556 40 58 CyaR 20 38 -15.09 0.0021103 0.7364947 glrK sensor protein kinase regulating glmY sRNA in two-component system with response regulator GlrR
b3770 36 54 CyaR 35 52 -14.65 0.0028743 0.779419 ilvE branched-chain amino acid aminotransferase
b3541 -74 -53 CyaR 14 30 -14.49 0.0032095 0.779419 dppD dipeptide/heme ABC transporter ATPas
b3456 45 74 CyaR 15 42 -14.38 0.0034603 0.779419 livM branched-chain amino acid ABC transporter permease
b0814 -9 26 CyaR 1 48 -14.33 0.0035802 0.779419 ompX outer membrane protein X
b1167 -41 -13 CyaR 4 33 -14.31 0.0036291 0.779419 ymgC Blue light low temperature and stress induced protein
b4350 -75 -45 CyaR 15 36 -14.19 0.0039361 0.7849708 hsdR endonuclease R Type I restriction enzyme
b4547 23 35 CyaR 34 46 -13.97 0.004561 0.8345133 ypfN putative membrane protein UPF0370 family
b0435 -63 -44 CyaR 21 36 -13.8 0.0051044 0.8345133 bolA stationary-phase morphogene transcriptional repressor for mreB also regulator for dacA dacC and ampC
b1250 28 58 CyaR 1 33 -13.78 0.0051721 0.8345133 kch voltage-gated potassium channel
b3197 10 40 CyaR 1 35 -13.72 0.0053801 0.8345133 kdsD D-arabinose 5-phosphate isomerase
b3879 -45 -26 CyaR 13 40 -13.58 0.0058953 0.8662988 yihR putative sulphoquinovose mutarotase
b3861 52 70 CyaR 31 49 -13.18 0.007625 0.9277422 yihF DUF945 family protein
b1579 -61 -38 CyaR 9 32 -13.17 0.0076736 0.9277422 intQ pseudogene Qin prophage phage integrase familyPhage or Prophage Related
b0704 -71 -37 CyaR 1 33 -13.16 0.0077225 0.9277422 ybfC putative secreted protein
b4342 -53 -28 CyaR 5 28 -12.97 0.0087074 0.9277422 yjiT pseudogene
b2568 40 60 CyaR 16 38 -12.94 0.0088729 0.9277422 lepB leader peptidase (signal peptidase I)
b2742 53 72 CyaR 24 44 -12.91 0.0090413 0.9277422 nlpD activator of AmiC murein hydrolase activity lipoprotein
b2859 -59 -36 CyaR 9 32 -12.89 0.0091552 0.9277422 ygeO pseudogene orgA family part of T3SS PAI ETT2 remnant
b3482 42 71 CyaR 1 35 -12.85 0.0093869 0.9277422 rhsB Rhs protein with DUF4329 family putative toxin domain putative neighboring cell growth inhibitor
b2957 43 68 CyaR 22 43 -12.83 0.0095047 0.9277422 ansB periplasmic L-asparaginase 2
b2308 -11 19 CyaR 2 36 -12.74 0.0100518 0.9277422 hisQ histidine ABC transporter permease
b1278 -56 -30 CyaR 10 41 -12.73 0.0101143 0.9277422 pgpB phosphatidylglycerophosphatase B
b1179 -75 -58 CyaR 16 32 -12.63 0.0107592 0.9277422 ycgL UPF0745 family protein
b1445 17 47 CyaR 1 33 -12.58 0.0110954 0.9277422 ydcX DUF2566 family protein
b1115 37 45 CyaR 9 17 -12.46 0.0119418 0.9277422 ycfT inner membrane protein
b2416 -14 10 CyaR 2 27 -12.38 0.0125381 0.9277422 ptsI PEP-protein phosphotransferase of PTS system (enzyme I)
b4595 -48 -34 CyaR 31 49 -12.33 0.0129245 0.9277422 yciY uncharacterized protein
b1615 -74 -64 CyaR 24 35 -12.16 0.0143201 0.9277422 uidC putative outer membrane porin for beta-glucuronides porin protein
b4513 25 54 CyaR 11 35 -12.16 0.0143201 0.9277422 kdpF potassium ion accessory transporter subunit
b1825 54 66 CyaR 37 49 -12.12 0.0146678 0.9277422 yebO putative inner membrane protein
b3423 37 59 CyaR 9 38 -12.11 0.0147559 0.9277422 glpR pseudogene DNA-binding transcriptional repressorregulator Energy metabolism carbon: Anaerobic respiration repressor of the glp operon
b3139 33 73 CyaR 1 39 -11.9 0.0167203 0.9277422 agaC N-acetylgalactosamine-specific enzyme IIC component of PTS
b3168 49 67 CyaR 29 45 -11.86 0.0171203 0.9277422 infB translation initiation factor IF-2
b4523 -72 -41 CyaR 15 49 -11.84 0.0173235 0.9277422 yciX uncharacterized protein
b2636 -57 -40 CyaR 9 23 -11.73 0.0184807 0.9277422 yfjS CP4-57 prophage uncharacterized protein
b1599 -11 21 CyaR 13 49 -11.69 0.0189186 0.9277422 mdtI multidrug efflux system transporter
b0764 -72 -62 CyaR 17 27 -11.66 0.0192531 0.9277422 modB molybdate ABC transporter permease chlorate resistance protein
b1628 65 73 CyaR 10 18 -11.62 0.0197074 0.9277422 rsxB SoxR iron-sulfur cluster reduction factor component putative iron-sulfur protein
b1607 28 62 CyaR 1 36 -11.6 0.0199382 0.9277422 ydgC GlpM family inner membrane protein
b1421 46 71 CyaR 23 47 -11.58 0.0201714 0.9277422 trg methyl-accepting chemotaxis protein III ribose and galactose sensor receptor
b0426 -75 -65 CyaR 30 40 -11.54 0.0206453 0.9277422 yajQ phage Phi6 host factor ATP/GTP binding protein
b1152 63 72 CyaR 30 39 -11.44 0.0218742 0.9277422 jayE pseudogene e14 prophagePhage or Prophage Related
b1363 41 55 CyaR 29 43 -11.43 0.0220007 0.9277422 trkG Rac prophage potassium transporter subunit
b1701 55 62 CyaR 10 17 -11.42 0.0221278 0.9277422 fadK short chain acyl-CoA synthetase anaerobic
b1041 54 73 CyaR 10 34 -11.4 0.022384 0.9277422 csgB curlin nucleator protein minor subunit in curli complex
b1891 40 52 CyaR 16 32 -11.35 0.0230363 0.9277422 flhC flagellar class II regulon transcriptional activator with FlhD
b0222 -56 -30 CyaR 18 46 -11.31 0.0235704 0.9277422 gmhA D-sedoheptulose 7-phosphate isomerase
b1956 -12 22 CyaR 16 49 -11.27 0.0241156 0.9277422 yedQ putative membrane-anchored diguanylate cyclase
b2377 -13 26 CyaR 1 50 -11.27 0.0241156 0.9277422 yfdY DUF2545 family putative inner membrane protein
b1824 -25 17 CyaR 2 43 -11.22 0.0248132 0.9277422 yobF DUF2527 family heat-induced protein
b3412 -55 -38 CyaR 23 40 -11.17 0.0255288 0.9277422 bioH pimeloyl-ACP methyl ester carboxylesterase
b0444 28 64 CyaR 23 49 -11.11 0.0264121 0.9277422 queC 7-cyano-7-deazaguanine (preQ0) synthase queuosine biosynthesis
b4686 -70 -59 CyaR 19 30 -11.09 0.0267126 0.9277422 yshB uncharacterized protein
b2721 -73 -43 CyaR 1 39 -11.06 0.0271691 0.9277422 hycE hydrogenase 3 large subunit
b3101 22 45 CyaR 19 46 -11.01 0.0279455 0.9277422 yqjF putative quinol oxidase subunit
b2174 60 70 CyaR 31 41 -10.95 0.0289036 0.9277422 lpxT lipid A 1-diphosphate synthase undecaprenyl pyrophosphate:lipid A 1-phosphate phosphotransferase
b1873 45 70 CyaR 11 49 -10.94 0.0290661 0.9277422 torY TMAO reductase III (TorYZ) cytochrome c-type subunit
b3105 24 45 CyaR 10 30 -10.91 0.0295585 0.9277422 yhaJ LysR family putative transcriptional regulator
b2085 -26 -11 CyaR 15 30 -10.89 0.029891 0.9277422 yegR uncharacterized protein
b3215 60 73 CyaR 36 51 -10.88 0.0300585 0.9277422 yhcA putative periplasmic chaperone protein
b2025 47 72 CyaR 25 47 -10.83 0.0309086 0.9277422 hisF imidazole glycerol phosphate synthase catalytic subunit with HisH
b0107 67 75 CyaR 40 48 -10.82 0.0310812 0.9277422 hofB T2SE secretion family protein P-loop ATPase superfamily protein
b2158 32 71 CyaR 1 35 -10.82 0.0310812 0.9277422 yeiH UPF0324 family inner membrane protein
b0694 -75 -66 CyaR 41 49 -10.81 0.0312546 0.9277422 kdpE response regulator in two-component regulatory system with KdpD
b3426 27 53 CyaR 23 50 -10.8 0.031429 0.9277422 glpD sn-glycerol-3-phosphate dehydrogenase aerobic FAD/NAD(P)-binding
b2939 64 73 CyaR 11 20 -10.76 0.032135 0.9277422 yqgB uncharacterized protein
b1784 -30 -20 CyaR 24 34 -10.69 0.0334048 0.9277422 yeaH UPF0229 family protein
b3492 28 49 CyaR 9 43 -10.65 0.0341505 0.9277422 yhiN putative oxidoreductase
b3075 30 38 CyaR 23 31 -10.65 0.0341505 0.9277422 ebgR transcriptional repressor
b4322 9 50 CyaR 1 48 -10.65 0.0341505 0.9277422 uxuA mannonate hydrolase
b3890 60 67 CyaR 29 36 -10.64 0.0343392 0.9277422 yiiF putative thymol sensitivity protein CopG family putative transcriptional regulator
b1739 15 35 CyaR 29 49 -10.63 0.0345289 0.9277422 osmE osmotically-inducible lipoprotein
b3284 -60 -47 CyaR 16 31 -10.6 0.0351035 0.9277422 smg DUF494 family putative periplasmic protein
b0465 33 50 CyaR 1 26 -10.58 0.0354913 0.9277422 mscK mechanosensitive channel protein intermediate conductance K+ regulated
b0684 -15 27 CyaR 1 48 -10.55 0.0360802 0.9277422 fldA flavodoxin 1
b2667 -64 -42 CyaR 20 48 -10.49 0.0372843 0.9277422 ygaV tributyltin-inducible repressor of ygaVP
b0412 56 67 CyaR 29 39 -10.47 0.0376936 0.9277422 yajI putative lipoprotein
b3600 54 72 CyaR 14 33 -10.46 0.0378997 0.9277422 mtlD mannitol-1-phosphate dehydrogenase NAD-dependent
b0675 61 74 CyaR 29 42 -10.45 0.0381068 0.9277422 umpH UMP phosphatase
b2036 -19 3 CyaR 17 38 -10.41 0.0389456 0.9277422 glf UDP-galactopyranose mutase FAD/NAD(P)-binding
b0698 -65 -36 CyaR 11 35 -10.39 0.0393711 0.9277422 kdpA potassium translocating ATPase subunit A
b4470 -58 -29 CyaR 17 45 -10.38 0.0395854 0.9277422 yhaM putative L-serine dehydratase alpha chain
b4463 -61 -51 CyaR 36 46 -10.37 0.0398007 0.9277422 ygcU putative FAD-linked oxidoreductase
b0140 -19 10 CyaR 3 33 -10.36 0.0400171 0.9277422 yadV putative periplasmic pilin chaperone
b4144 -25 -8 CyaR 15 32 -10.34 0.040453 0.9277422 yjeI DUF4156 family lipoprotein
b1220 58 71 CyaR 25 36 -10.33 0.0406726 0.9277422 ychO putative invasin
b4040 30 39 CyaR 21 30 -10.32 0.0408932 0.9277422 ubiA p-hydroxybenzoate octaprenyltransferase
b0886 47 75 CyaR 24 49 -10.31 0.0411148 0.9277422 cydC glutathione/cysteine ABC transporter export permease/ATPase
b0607 -14 -8 CyaR 63 69 -10.28 0.0417863 0.9277422 uspG universal stress protein UP12
b3535 -30 -21 CyaR 27 36 -10.28 0.0417863 0.9277422 yhjR DUF2629 family protein
b0989 -32 -16 CyaR 20 35 -10.27 0.0420123 0.9277422 cspH stress protein member of the CspA-family
b2131 33 47 CyaR 1 16 -10.25 0.0424675 0.9277422 osmF putative ABC transporter periplasmic binding protein

Details of Selected Interaction Download Interaction Details 

Target

Query


		

		

		

		

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

			

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
			

		
 
		
		

		
		

		
		

			

		

		
		

	

	
	
	
	
	
	
	




			 
	





	
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